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nautilus-gksu incorrectly invokes MIME handlers with commandline parameters. This includes opening folders in Nautilus with special options - and it is so in a default GNOME installation, --no-desktop parameter is passed.
How to reproduce:
0. Pre-requisites: an ordinary GNOME session, nautilus-gksu-2.0.2 is installed
1. Switch off Nautilus desktop in GNOME (i.e., switch off the GConf key /apps/nautilus/preferences/show_desktop). Icons on your desktop should disappear.
2. Make sure no Nautilus processes run.
3. Now run Nautilus: nautilus --no-desktop
4. Pick some directory/folder and 'Open as administrator' it. Type the password as requested by gksu.
5. Nautilus window opens and(!) a Nautilus desktop activates (icons appear and even the background may change, according to root's preferences).
The cause of the problem is using g_app_info_get_executable() instead of g_app_info_get_commandline(). The attached patch fixes things.